Disease Clusters?

Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.

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Cluster 199

8 diseases · 10 shared-gene connections
8 Diseases
9 Unique genes
0.219 Avg. similarity score
Hypertyrosinemia Most-connected disease (5 links)
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Disease Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details · click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) · drag a node to pin it in place · scroll/pinch to zoom.

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Hypertyrosinemia 5 5 4
Tyrosinemia 4 4 4
Beta-mannosidosis 3 3 4
tyrosinemia type I 3 3 1
tyrosinemia type II 2 2 1
ALS2-related motor neuron disease 1 1 1
Usher syndrome type 2 1 1 2
glutaryl-CoA dehydrogenase deficiency 1 1 1

Top shared genes (genes linked to 2+ member diseases)

Gene ⇵ Member diseases ⇵ Linked diseases
FAH 4 / 8 Beta-mannosidosis, Hypertyrosinemia, Tyrosinemia, tyrosinemia type I
TAT 3 / 8 Hypertyrosinemia, Tyrosinemia, tyrosinemia type II
ADGRV1 2 / 8 Beta-mannosidosis, Usher syndrome type 2
ALS2 2 / 8 ALS2-related motor neuron disease, Hypertyrosinemia
GCDH 2 / 8 glutaryl-CoA dehydrogenase deficiency, Tyrosinemia
HPD 2 / 8 Hypertyrosinemia, Tyrosinemia
What do these columns mean?
Connections in cluster
How many other members this disease has a shared-gene link to (the node size in the network above). The most-connected diseases are the cluster's core.
Significant partners
How many of those links are statistically significant (FDR q < 0.05).
Curated genes
Distinct curated genes linked to that disease in GeDiPNet.
Member diseases (Top shared genes)
How many of this cluster's diseases are linked to the gene, out of the cluster's total. Genes shared by many members are the most direct explanation of why they group together.
Overlap genes (x / y)
x = genes shared between this cluster and the pathway/GO term; y = that pathway/GO term's total gene count. A higher x relative to y (and to the cluster's own size) means a tighter biological match.
Cluster gene count
Total distinct genes across every disease in this cluster -- the "n" used in the significance test below.
Fold enrichment
Observed overlap divided by the overlap expected by chance, given the cluster's gene count, the pathway/term's size and the gene universe tested. 5× means five times more shared genes than random. Tells strong hits apart when q-values are all vanishingly small.
P-value / FDR q-value
Is this pathway/GO term's overlap with the cluster more than chance? Upper-tail hypergeometric test, Benjamini-Hochberg corrected across every tested pathway/term (prefer the q-value -- it accounts for testing many at once).
Shared genes (Pairs within this cluster)
Number of curated genes the two diseases in that row have in common.
Similarity score (Pairs within this cluster)
Jaccard-based gene overlap between the two specific diseases in that row -- same metric as the main Shared-Gene Disease Pairs page.

Enriched Pathways (why this cluster is grouped, biologically)

Pathway ⇵ Source ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
Tyrosine catabolism
FAH, HPD, TAT
 Reactome 3 / 5 801× 2.91e-9 2.90e-7 ✓ sig.
Tyrosine metabolism
FAH, HPD, TAT
 KEGG 3 / 36 111× 2.05e-6 8.99e-5 ✓ sig.
Ubiquinone and other terpenoid-quinone biosynthesis
HPD, TAT
 KEGG 2 / 12 222× 3.28e-5 9.00e-4 ✓ sig.
Phenylalanine metabolism
HPD, TAT
 KEGG 2 / 16 167× 5.96e-5 1.47e-3 ✓ sig.
Lysosomal oligosaccharide catabolism
MANBA
 Reactome 1 / 4 334× 2.99e-3 3.07e-2 ✓ sig.
Phenylalanine, tyrosine and tryptophan biosynthesis
TAT
 KEGG 1 / 6 222× 4.49e-3 4.08e-2 ✓ sig.
Lysine catabolism
GCDH
 Reactome 1 / 12 111× 8.96e-3 6.42e-2
Other glycan degradation
MANBA
 KEGG 1 / 18 74.1× 1.34e-2 8.14e-2
Metabolic pathways
FAH, HPD, TAT, GCDH
 KEGG 4 / 1,563 3.4× 2.09e-2 1.06e-1
Tryptophan metabolism
GCDH
 KEGG 1 / 42 31.8× 3.10e-2 1.31e-1
Fatty acid degradation
GCDH
 KEGG 1 / 43 31.0× 3.18e-2 1.33e-1
Cysteine and methionine metabolism
TAT
 KEGG 1 / 52 25.7× 3.83e-2 1.48e-1
Lysine degradation
GCDH
 KEGG 1 / 63 21.2× 4.62e-2 1.64e-1
RAB GEFs exchange GTP for GDP on RABs
ALS2
 Reactome 1 / 90 14.8× 6.55e-2 1.98e-1
Lysosome
MANBA
 KEGG 1 / 133 10.0× 9.54e-2 2.41e-1

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
L-tyrosine catabolic process
FAH, HPD, TAT
 GO:0006572 3 / 6 1,038× 1.54e-9 3.30e-7 ✓ sig.
L-phenylalanine catabolic process
FAH, HPD, TAT
 GO:0006559 3 / 8 779× 4.32e-9 8.18e-7 ✓ sig.
aromatic amino acid metabolic process
FAH, HPD, TAT
 GO:0009072 3 / 10 623× 9.25e-9 1.60e-6 ✓ sig.
sensory perception of light stimulus
ADGRV1, CDH23, USH2A
 GO:0050953 3 / 13 479× 2.20e-8 3.40e-6 ✓ sig.
photoreceptor cell maintenance
ADGRV1, CDH23, USH2A
 GO:0045494 3 / 45 138× 1.09e-6 8.86e-5 ✓ sig.
maintenance of animal organ identity
ADGRV1, USH2A
 GO:0048496 2 / 5 831× 2.06e-6 1.47e-4 ✓ sig.
inner ear receptor cell differentiation
ADGRV1, USH2A
 GO:0060113 2 / 9 461× 7.41e-6 4.11e-4 ✓ sig.
inner ear auditory receptor cell differentiation
CDH23, USH2A
 GO:0042491 2 / 19 219× 3.51e-5 1.38e-3 ✓ sig.
sensory perception of sound
ADGRV1, CDH23, USH2A
 GO:0007605 3 / 162 38.5× 5.17e-5 1.85e-3 ✓ sig.
inner ear receptor cell stereocilium organization
ADGRV1, CDH23
 GO:0060122 2 / 25 166× 6.15e-5 2.10e-3 ✓ sig.
visual perception
ADGRV1, CDH23, USH2A
 GO:0007601 3 / 215 29.0× 1.20e-4 3.47e-3 ✓ sig.
establishment of protein localization
ADGRV1, USH2A
 GO:0045184 2 / 51 81.4× 2.60e-4 6.08e-3 ✓ sig.
inner ear development
ADGRV1, CDH23
 GO:0048839 2 / 54 76.9× 2.91e-4 6.57e-3 ✓ sig.
homogentisate catabolic process
FAH
 GO:1902000 1 / 1 2,076× 4.82e-4 9.31e-3 ✓ sig.
aromatic amino acid family catabolic process
TAT
 GO:0009074 1 / 1 2,076× 4.82e-4 9.31e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hypertyrosinemia Tyrosinemia 0.500 3 2.63e-11 2.94e-10 ✓ sig.
ALS2-related motor neuron disease Hypertyrosinemia 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Beta-mannosidosis tyrosinemia type I 0.200 1 2.60e-4 6.40e-4 ✓ sig.
glutaryl-CoA dehydrogenase deficiency Tyrosinemia 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Hypertyrosinemia tyrosinemia type I 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Tyrosinemia tyrosinemia type I 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Hypertyrosinemia tyrosinemia type II 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Tyrosinemia tyrosinemia type II 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Beta-mannosidosis Usher syndrome type 2 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Beta-mannosidosis Hypertyrosinemia 0.125 1 1.04e-3 1.72e-3 ✓ sig.